Compensatory mutations suggest that base-pairing with a small nuclear RNA is required to form the 3′ end of H3 messenger RNA

Nature ◽  
1986 ◽  
Vol 323 (6091) ◽  
pp. 777-781 ◽  
Author(s):  
Fred Schaufele ◽  
Gregory M. Gilmartin ◽  
Willi Bannwarth ◽  
Max L. Birnstiel
Keyword(s):  
Messenger Rna ◽  
Small Nuclear Rna ◽  
Base Pairing ◽  
Nuclear Rna ◽  
Compensatory Mutations

scholarly journals Structural analyses of the 7SK ribonucleoprotein (RNP), the most abundant human small RNP of unknown function.

1991 ◽  
Vol 11 (7) ◽  
pp. 3432-3445 ◽  
Author(s):  
D A Wassarman ◽  
J A Steitz
Keyword(s):  
Secondary Structure ◽  
Rnase H ◽  
Small Nuclear Rna ◽  
Base Pairing ◽  
Structural Determinants ◽  
Nuclear Rna ◽  
Sequence Complementarity ◽  
Associated Proteins ◽  
Stem Structure

The human 7SK ribonucleoprotein (RNP) has been analyzed to determine its RNA secondary structure and protein constituents. HeLa cell 7SK RNA alone and within its RNP have been probed by chemical modification and enzymatic cleavage, and sites of modification or cleavage have been mapped by primer extension. The resulting secondary structure suggests that structural determinants necessary for capping (a 5' stem followed by the sequence AUPuUPuC) and nuclear migration (the sequence AUPuUPuC) of 7SK RNA may be similar to those for U6 small nuclear RNA (snRNA). It also supports existence of a 3' stem structure which could serve to self-prime cDNA synthesis during pseudogene formation. Oligonucleotide-directed RNase H digestion indicated regions of 7SK RNA capable of base pairing with other nucleic acids. Antisense 2'-O-methyl RNA oligonucleotides were used to affinity select the 7SK RNP from an in vivo 35S-labeled cell sonic extract and identify eight associated proteins of 83, 48, 45, 43, 42, 21, 18, and 13 kDa. 7SK RNA has extensive sequence complementarity to U4 snRNA, within the U4/U6 base pairing domain, and also to U11 snRNA. The possibility that the 7SK RNP is an unrecognized component of the pre-mRNA processing machinery is discussed.

Structural analyses of the 7SK ribonucleoprotein (RNP), the most abundant human small RNP of unknown function

1991 ◽  
Vol 11 (7) ◽  
pp. 3432-3445
Author(s):  
D A Wassarman ◽  
J A Steitz
Keyword(s):  
Secondary Structure ◽  
Rnase H ◽  
Small Nuclear Rna ◽  
Base Pairing ◽  
Structural Determinants ◽  
Nuclear Rna ◽  
Sequence Complementarity ◽  
Associated Proteins ◽  
Stem Structure

The human 7SK ribonucleoprotein (RNP) has been analyzed to determine its RNA secondary structure and protein constituents. HeLa cell 7SK RNA alone and within its RNP have been probed by chemical modification and enzymatic cleavage, and sites of modification or cleavage have been mapped by primer extension. The resulting secondary structure suggests that structural determinants necessary for capping (a 5' stem followed by the sequence AUPuUPuC) and nuclear migration (the sequence AUPuUPuC) of 7SK RNA may be similar to those for U6 small nuclear RNA (snRNA). It also supports existence of a 3' stem structure which could serve to self-prime cDNA synthesis during pseudogene formation. Oligonucleotide-directed RNase H digestion indicated regions of 7SK RNA capable of base pairing with other nucleic acids. Antisense 2'-O-methyl RNA oligonucleotides were used to affinity select the 7SK RNP from an in vivo 35S-labeled cell sonic extract and identify eight associated proteins of 83, 48, 45, 43, 42, 21, 18, and 13 kDa. 7SK RNA has extensive sequence complementarity to U4 snRNA, within the U4/U6 base pairing domain, and also to U11 snRNA. The possibility that the 7SK RNP is an unrecognized component of the pre-mRNA processing machinery is discussed.

scholarly journals Analysis of aberrant pre-messenger RNA splicing resulting from mutations inATP8B1and efficientin vitrorescue by adapted U1 small nuclear RNA

Hepatology ◽  
2015 ◽  
Vol 61 (4) ◽  
pp. 1382-1391 ◽  
Author(s):  
Wendy L. van der Woerd ◽  
Johanna Mulder ◽  
Franco Pagani ◽  
Ulrich Beuers ◽  
Roderick H.J. Houwen ◽  
...  
Keyword(s):  
Rna Splicing ◽  
Messenger Rna ◽  
Small Nuclear Rna ◽  
Nuclear Rna

scholarly journals Base pairing interactions between substrate RNA and H/ACA guide RNA modulate the kinetics of pseudouridylation, but not the affinity of substrate binding by H/ACA small nucleolar Ribonucleoproteins

2019 ◽  
Author(s):  
Erin Katelyn Kelly ◽  
Dominic Philip Czekay ◽  
Ute Kothe
Keyword(s):  
Messenger Rna ◽  
Ribosome Biogenesis ◽  
Small Nuclear Rna ◽  
Base Pairing ◽  
Base Pairs ◽  
Guide Rna ◽  
Guide Rnas ◽  
Pairing Strength ◽  
Pairing Interactions ◽  
Time Courses

AbstractH/ACA small nucleolar ribonucleoproteins (snoRNPs) pseudouridylate RNA in eukaryotes and archaea. They target many RNAs site-specifically through base-pairing interactions between H/ACA guide and substrate RNA. Besides ribosomal RNA (rRNA) and small nuclear RNA (snRNA), H/ACA snoRNPs are thought to also modify messenger RNA (mRNA) with potential impacts on gene expression. However, the base-pairing between known target RNAs and H/ACA guide RNAs varies widely in nature, and therefore the rules governing substrate RNA selection are still not fully understood. To provide quantitative insight into substrate RNA recognition, we systematically altered the sequence of a substrate RNA target by the Saccharomyces cerevisiae H/ACA guide RNA snR34. Time courses measuring pseudouridine formation revealed a gradual decrease in the initial velocity of pseudouridylation upon reducing the number of base pairs between substrate and guide RNA. Changing or inserting nucleotides close to the target uridine severely impairs pseudouridine formation. Interestingly, filter binding experiments show that all substrate RNA variants bind to H/ACA snoRNPs with nanomolar affinity. Next, we showed that binding of inactive, near-cognate RNAs to H/ACA snoRNPs does not inhibit their activity for cognate RNAs, presumably because near-cognate RNAs dissociate rapidly. We discuss that the modulation of initial velocities by the base pairing strength might affect the order and efficiency of pseudouridylation in rRNA during ribosome biogenesis. Moreover, the binding of H/ACA snoRNPs to near-cognate RNAs may be a mechanism to search for cognate target sites. Together, our data provide critical information to aid in the prediction of productive H/ACA guide – substrate RNA pairs.

How Is Precursor Messenger RNA Spliced by the Spliceosome?

2020 ◽  
Vol 89 (1) ◽  
pp. 333-358 ◽  
Author(s):  
Ruixue Wan ◽  
Rui Bai ◽  
Xiechao Zhan ◽  
Yigong Shi
Keyword(s):  
Active Site ◽  
Rna Splicing ◽  
Messenger Rna ◽  
Small Nuclear Rna ◽  
Exon Ligation ◽  
Nuclear Rna ◽  
Catalytic Metal ◽  
Protein Components ◽  
Intron Removal ◽  
Duplex Formation

Splicing of the precursor messenger RNA, involving intron removal and exon ligation, is mediated by the spliceosome. Together with biochemical and genetic investigations of the past four decades, structural studies of the intact spliceosome at atomic resolution since 2015 have led to mechanistic delineation of RNA splicing with remarkable insights. The spliceosome is proven to be a protein-orchestrated metalloribozyme. Conserved elements of small nuclear RNA (snRNA) constitute the splicing active site with two catalytic metal ions and recognize three conserved intron elements through duplex formation, which are delivered into the splicing active site for branching and exon ligation. The protein components of the spliceosome stabilize the conformation of the snRNA, drive spliceosome remodeling, orchestrate the movement of the RNA elements, and facilitate the splicing reaction. The overall organization of the spliceosome and the configuration of the splicing active site are strictly conserved between human and yeast.

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